The data has been analyzed. The scan information from corresponding NIFTI
file as following:
nua502608:3T8619 kding$ mri_info 3T8619_T1.nii.gz
Volume information for 3T8619_T1.nii.gz
type: nii
dimensions: 160 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 160.000
dof: 0
xstart: -80.0, xend: 80.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r =
0.0107
: x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a =
7.8592
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s =
-15.4014
Orientation : LPS
Primary Slice Direction: axial
voxel to ras transform:
-1.0000 -0.0000 -0.0000 80.0107
-0.0000 -1.0000 -0.0000 135.8592
0.0000 0.0000 1.0000 -143.4014
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
-1.0000 0.0000 0.0000 80.0107
0.0000 -1.0000 0.0000 135.8592
0.0000 0.0000 1.0000 143.4014
0.0000 0.0000 0.0000 1.0000
Date: Thu, 5 Apr 2018 12:59:16 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] scan log generated by dcmunpack
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <22ecfa88-e463-169b-03c5-4c25ac224...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed
It looks like there is something wrong with that dicom file/series
because the pixel spacing is "unknown". Where did the dicoms from from?
Have they been anonymized?
On 04/05/2018 12:12 PM, Kan Ding wrote:
>Hello:
>
>I am trying to unpack my DICOM folder and run recon-all. After
>dcmunpack, I selected 301 to run recon-all. But the recon-all didn?t
>go through. Please see the attached scan.log, recon-all.log,
>error.log, and the pic of my DICOM folder.
>
>Thank you so mch.
>
>Kan Ding, MD
>
On 4/5/18, 3:21 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu"
<reesurfer-boun...@nmr.mgh.harvard.edu on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu> wrote:
>Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
>To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/istinfo/freesurfer
>or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
>You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of Freesurfer digest..."
>
>
>Today's Topics:
>
> 1. scan log generated by dcmunpack (Kan Ding)
> 2. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (Bruce Fischl)
> 3. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (srishti goel)
> 4. Qdec+Table format issue ????? (Dimitrios Trifonopoulos)
> 5. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (Bruce Fischl)
> 6. Re: recon-all: exited with errors (whit matter peak at 110,
> cannot allocate memory) (srishti goel)
> 7. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (Bruce Fischl)
> 8. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (srishti goel)
> 9. Re: recon-all: exited with errors (white matterpeak at 110,
> cannot allocate memory) (Bruce Fischl)
> 10. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (srishti goel)
> 11. Re: recon-all: exited with errors (white matter peak at 110,
> cannot allocate memory) (Bruce Fischl)
> 12. Re: mri_vol2surf: unable to compare volume maps (Douglas N. Greve)
> 13. Re: scan log generated by dcmunpack (Douglas N. Greve)
> 14. Time Series to Surface (Crawford, Anna)
> 15. Tracula - Could not find satisfactory control point fit
> (Lussier,Desiree)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 5 Ap 2018 16:12:43 +0000
>From: Kan Ding <kan.d...@utsouthwestern.edu>
>Subject: [Freesurfer] scan log generated by dcmunpack
>To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>Message-ID: <d6ebc339.10ff3%kan.d...@utsouthwestern.edu>
>Contnt-Type: text/plain; charset="iso-8859-1"
>
>Hello:
>
>I am trying to unpack my DICOM folder and run recon-all. After dcmunpack,
>I selected 301 to run recon-all. But the recon-all didn't go through.
>Please see the attached scan.log, recon-all.log, error.log, and the pic
>of my DICOM folder.
>
>Thank you so much.
>Kan Din, MD
>Assistant Professor- Department of Neurology and Neurotherapeutics
>UT Southwestern Medical Center at Dallas
>Tel: 214-648-9197
>Fax: 214-648-6320
>
>________________________________
>
>UT Southwestern
>
>
>Medical Center
>
>
>
>The future of medicine, today.
>
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>
>------------------------------
>
>Message: 2
>Date: Thu, 5 Apr 2018 12:16:26 -0400 (EDT)
>From: Bruce Fischl <fi...@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfersupport list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <alpine.lrh.2.21.1804051215360.18...@tiamat.nmr.mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Srishti
>
>are you sure that your machine didn't just run out of memory? The
>recon-all.log file includes the amount of free (and total) memory at the
>timethe process was started.
>
>cheers
>Bruce
>
> On Thu, 5 Apr
>2018, srishti goel wrote:
>
>> Hi,
>> I have been trying to edit structural brains and very few times I wuld
>>get the following error while running recon-all -s
>> subjID
>>
>> white matter peak fond at 110
>> cannot allocate memory
>>
>> Upon looking at the archive, tere was only one similar issue and it
>>was recommend to check mri_info as the brain mask might
>> have been corrupted. I did that and here is the output:
>>
>> olume information for brainmask.mgz
>>
>> ? ? ? ? ? type: MGH
>>
>> ? ? dimensions: 256 x 256 x 256
>>
>> ?? voxel sizes: 1.000000, 1.000000, 1.000000
>>
>> ? ? ? ? ? type: UCHAR (0)
>>
>> ?? ? ? ? ? fov: 256.000
>>
>> ?? ? ? ? ? dof: 0
>>
>> ? ? ? ? xstart: -128.0, xend: 128.0
>>
>> ? ? ? ? ystart: -128.0, yend: 128.0
>>
>> ? ? ? ? zstart: -128.0, zend: 128.0
>>
>> ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
>>0.00 degrees
>>
>> ?? ? ? nframes: 1
>>
>> ?? ? ? PhEncDir: UNKNOWN
>>
>> ?? ? ? FieldStrength: 0.000000
>>
>> ras xform present
>>
>> ? ? xform info: x_r =? -1.0000, y_r = ? 0.0000, z_r = ? .0000, c_r =?
>>? -1.0000
>>
>> ? ? ? ? ? ? ? : x_a = ? 0.0000, y_a = ? 0.0000, z_a = ? 1.0000, c_a =?
>>? 37.500
>>
>> ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s =? -1.0000, z_s = ? 0.0000, c_s = ?
>>? 4.7185
>>
>>
>> talairach xfm :
>>/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tala
>>irach.xfm
>>
>> Orientation ? : LIA
>>
>> Primary Slice Direction: coronal
>>
>>
>> voxel to ras transform:
>>
>> ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? 0.0000? 127.0000
>>
>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 1.0000 ? -90.5000
>>
>> ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? 0.0000 ? 132.7185
>>
>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? 1.0000
>>
>>
>> voxel-to-ras determinant -1
>>
>>
>> ras to voxel transform:
>>
>> ?? ? ? ? ? ? ? -1.0000? -0.0000? -0.0000 ? 127.0000
>>
>> ?? ? ? ? ? ? ? -0.0000? -0.0000? -1.000 ? 132.7185
>>
>> ?? ? ? ? ? ? ? -0.0000 ? 1.0000? -0.0000? ? 90.5000
>>
>> ?? ? ? ? ? ? ? -0.0000? -0.0000? -0.0000 ? ? 1.0000
>>
>>
>> Is there any other ay to resolve this issue than reconstruction the
>>brain again and doing all the edits all over again hoping
>> that the?brain mask does not get corrupted this time?
>>
>> Appreciate any help with this.
>>
>> Best,
>> Srishti
>>
>>
>
>------------------------------
>
Message: 3
>Date: Thu, 5 Apr 2018 12:19:06 -0400
>From: srishti goel <23srishtigoel@gmailcom>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <CAGqM=zimvc9-jevnkodro2jeo8nwmbytmxbbd4qexnkedu...@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Bruce,
>
>The machine definitely hasn't run out of memory. Here is the memory usage
>from recon-all.log
>
> total used free
>shared buff/cache available
>Mem: 263726968 34330048 152102696 12944 77294224
>191963372
>Swap: 2097148 0 2097148
>
>
>
>
>Best,
>Srishti
>Soial/Clinical Research Specialist
>Child Imaging Research and Life Experiences Lab
>University of North Carolina at Chapel Hill
>email (W): srish...@email.unc.edu
>skype: srishti.goel12
>
>
>On Thu, Apr 5, 218 at 12:16 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>wrote:
>
>> Hi Srishti
>>
>> are you sure that your machine didn't just run out of memry? The
>> recon-all.log file includes the amount of free (and total) memory at the
>> time the processwas started.
>>
>> cheers
>> Bruce
>>
>>
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi,
>>> I have been trying to edit structural brains and very few times I would
>>> get the following error while running recon-all -s
>>> subjID
>>>>>> white matter peak found at 110
>>> cannot allocate memory
>>>
>>> Upon looking at the archive, there was only one similar issue and it
>>>was
>>> recommed to check mri_info as the brain mask might
>>> have been corrupted. I did that and here is the output
>>>
>>> Volume information for brainmask.mgz
>>>
>>> type: MGH
>>>
>>> dimensions: 256 x 256 x 256
>>>
>>> voxel sizes: 1.000000, 1.000000, 1.000000
>>>
>>> type: UCHAR (0)
>>>
>>> fov: 256.000
>>>
>>> dof: 0
>>>
>>> xstart: -128.0, xend: 128.0
>>>
>>> ystart: -128.0, yend: 128.0
>>
>>> zstart: -128.0, zend: 128.0
>>>
>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
>>>0.00
>>> degrees
>>>
>>> nframes: 1
>>
>>> PhEncDir: UNKNOWN
>>>
>>> FieldStrength: 0.000000
>>>
>>> rasxform present
>>>
>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
>>> -1.0000
>>>>>> : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
>>> 37.5000
>>>
>>> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
>>> 4.7185
>>>
>>>
>>> talairach xfm : /pine/scr/s/r/srishtig/Duke_Te
>> st/Freesurfer_out/11039/mri/transforms/talairach.xfm
>>>
>>> Orientation : LIA
>>>
>>> rimary Slice Direction: coronal
>>>
>>>
>>> voxel to ras transform:
>>>
>>> -.0000 0.0000 0.0000 127.0000
>>>
>>> 0.0000 0.0000 1.0000 -905000
>>>
>>> 0.0000 -1.0000 0.0000 132.7185
>>>
>>> 0.0000 0.0000 0.0000 1.0000
>>>
>>>
>>> voxel-to-ras determinant -1
>>>
>>>
>>> ras to voxel transform:
>>>
>>> -1.0000 -0.0000 -0.0000 127.0000
>>>
>>> -0.0000 -0.0000 -1.0000 132.7185
>>>
>>> 0.0000 1.0000 -0.0000 90.5000
>>>
>>> -0.0000 -0.0000 -0.0000 1.0000
>>>
>>>
>>> Is there any other way to resolve this issue than reonstruction the
>>> brain again and doing all the edits all over again hoping
>>> that the brain mask des not get corrupted this time?
>>>
>>> Appreciate any help with this.
>>>
>>> Best,
>>>Srishti
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> freesr...@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it
>> is
>> addressed If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, pleae contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
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>
>-----------------------------
>
>Message: 4
>Date: Thu, 5 Apr 2018 16:12:26 +0000
>From: Dimitrios Trifonopoulos <trif...@otmail.com>
>Subject: [Freesurfer] Qdec+Table format issue ?????
>To: "freesurfer@nmr.mgh.harvard.edu" <freesr...@nmr.mgh.harvard.edu>
>Message-ID:
> <AM5PR0701MB2291CD465CB533E255D8BFDF90BB0@AM5PR0701MB2291.eurprd07prod.o
>utlook.com>
>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Dear Recipient,
>
>
>I am a aster student new comer in FS. I am trying toi use the QDEC ti
>analyse some longitudinal data. Most probably my issue is related with
>the file format. I tried to use several txt editors (mac text editor,
>gedit and text wrangler) however I end up in 2 different errors without
>be abe to overcome the issue.
>
>The 1st error was:
>
>
> ERROR: qdec table missing correct column headers?
>
> Make sure first column is labeled 'fsid' for the time point and
>
> second column is 'fsid-base' t specify the subject tempate
>(base), e.g.:
>
>
> fsid fsid-base age
>
> me1 me 22.3
>
> me2 me 23.2
>
> you1 you 21.6
>
> you2 you 22.5
>
>
>Simones-iMac:subects SLMAC14$ long_mris_slopes --qdec
>/Applications/freesurfer/subjects/qdec/lala copy.dat.doc --meas tickness
>--hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
>-time years --qcache fsaverage --sd /Applications/freesurfer/subjects/
>
>
>and the 2nd one was:
>
>
>Parsing the qdec table:
>/Applications/freesurfer/subjects/qec/qdec.table.dat
>
>ERROR: qdec table /Applications/freesurfer/subjects/qdec/qdec.table.dat
>not found or empty?
>
>
>Even if I found a similar error im the forum, I didn't undestand finally
>how this guy overcome it. I also attached you the 2 files that I used.
>Please answer me as soon as you are available. Thank you
>
>
>All the Best,
>
>Dimitris
>
>
>
>
>
>
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>
>------------------------------
>
>Message: 5
>Date: Th, 5 Apr 2018 12:24:42 -0400 (EDT)
>From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <alpine.lrh.2.20.1804051224100.9...@gate.nmr.mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"
>
>if ou run the command that failed again on the command line directly
>(that
>is, not in recon-all) does it fail again?
>
>On Thu, 5 Apr 2018, srishi goel wrote:
>
>> Hi Bruce,
>>
>> The machine definitely hasn't run out of memory. Here is the memory
>usage
>> from recon-all.log ?
>>
>> ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? ? ?used ? ? ? ?free ? ? ? ? ? ??
>>? ?
>> shared ?buff/cache ? available
>> Mem: ? ? ?263726968 ? ?34330048 ? 152102696 ? ? ? 12944 ? ?77294224
>> 191963372
>> Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? ? ? ? ? 2097148
>>
>>
>>
>>
>> Best,
>> Srisht
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu>
>> wrote:
>> Hi Srishti
>>
>> are you sure that your machine didn't just run out of memory?
>> The recn-all.log file includes the amount of free (and total)
>> memory at the time the process as started.
>>
>> cheers
>> Bruce
>>
>> ?On Thu, 5 Apr 2018, srishti goel wrot:
>>
>> Hi,
>> I have been trying to edit structural brains and
>> very few times I would get the following error while
>> running recon-all -s
>> subjID
>>
>> white matter peak found at 110
>> cannot allocate memory
>>
>> Upon looking at the archive, there was only one
>> similar issue and it was recommend to check mri_info
>> as the brain mask might
>> have been corrupted. I did that and here is te
>> output:
>>
>> Volume information for brainmask.mgz
>>>> ? ? ? ? ? type: MGH
>>
>> ? ? dimensions: 256 x 256 x 56
>>
>> ?? voxel sizes: 1.000000, 1.000000, 1.000000
>>
>> ? ? ? ? type: UCHAR (0)
>>
>> ?? ? ? ? ? fov: 256.000
>>
>> ?? ? ? ? dof: 0
>>
>> ? ? ? ? xstart: -128.0, xend: 128.0
>>
>> ? ? ? ? ystart: -128.0, yend: 128.0
>>
>> ? ? ? ? zstart: -128.0, zend: 128.0
>>
>> ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00
>> msec, flip angle: 0.00 degrees
>>
>> ?? ? ? nframes: 1
>>
>> ?? ? ? PhEncDir: UNKNOWN
>>
>> ?? ? ? FieldStrength: 0.000000
>>
>> ras xform present
>>
>> ? ? xform info: x_r =? -1.0000 y_r = ? 0.0000, z_r
>> = ? 0.0000, c_r =? ? -1.0000
>>
>> ? ? ? ? ? ? ? : x_a = ? 0.000, y_a = ? 0.0000, z_a
>> = ? 1.0000, c_a =? ? 37.5000
>>
>> ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s =? -1.0000, z_s
>> = ? 0.0000, c_s = ? ? 4.7185
>>
>>
>> alairach xfm
>>:/pine/scr/s/r/srishtig/Duke_Test/Freesurfr_out/11039/mri/transforms/tal
>>air
>> ach.xfm
>>
>> Orientation ? : LIA
>>
>> Primary Slice Direction: coronal
>>
>>
>> voxel to ras transform:
>>
>> ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? 0.0000 ? 127.0000
>>
>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 1.0000 ? -9.5000
>>
>> ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? 0.0000 ? 132.7185
>>
>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 00000 ? ? 1.0000
>>
>>
>> voxel-to-ras determinant -1
>>
>>
>> ras to voxel transform:
>>
>> ?? ? ? ? ? ? -1.0000? -0.0000? -0.0000 ? 127.0000
>>
>> ?? ? ? ? ? ? ? 0.0000? -0.0000? -1.0000 ? 132.7185
>>
>> ?? ? ? ? ? ? -0.0000 ? 1.0000? -0.0000? ? 90.5000
>>
>> ?? ? ? ? ? ? ? -0.0000? -0.0000? -0.0000 ? ? 1.0000
>>
>>
>> Is there any other way to resolve this issue than
>> reconstruction the brain again and doing all the
>> edits all over again hoping
>> that the?brain mask does not get corrupted this
>> time?
>>
>> Appreciate any help with this.
>>
>> Best,
>> Srishti
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mai was sent to you in error and the
>> e-mail
>> contains patient informatin, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but dos not contain patient information, please contact the sender
>> and proprly
>> dispose of the e-mail.
>>
>>
>>
>>
>
>-----------------------------
>
>Message: 6
>Date: Thu, 5 Apr 2018 12:29:48 -0400
>From: srishti goel <23srishtig...@gmail.com>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <CAGqM=zgn1hmae0_nzurz1p-t3jr2syx-j1v4+hzoetz_nx9...@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>I am sorry, I am not sure what do you mean by running the command line
>directly?
>
>I use the following command:
>
>sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>srish...@email.unc.edu --wrap "export
>SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa"
>
>
>where sbatch..... until export is our local server submission command and
>I
>run this command from the command line itself, not using any script.
>
>Best,
>Srishti
>Social/Clinical Research Specialist
>Child Imaging Research and Life Experiences Lab
>University of North Caolina at Chapel Hill
>email (W): srish...@email.unc.edu
>skype: srishti.gel12
>
>
>On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harard.edu>
>wrote:
>
>> if you run the command that failed again on the cmmand line directly
>> (that is, not in recon-all) does it fail again?
>>
>>
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi Bruce,
>>>
>>> The machine definitely hasn't run out of memory. Here is the memory
>>>usage
>>> from recon-all.log
>>>
>>> total used free
>>> shared buff/cache available
>>> Mem: 263726968 34330048 152102696 12944 77294224
>>> 191963372
>>> Swap: 2097148 0 207148
>>>
>>>
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical ResearchSpecialist
>>> Child Imaging Research and Life Experiences Lab
>>> Univrsity of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.ed
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:16 PM, ruce Fischl
>>><fis...@nmr.mgh.harvard.edu
>>> >
>>> wrote:
>>> Hi rishti
>>>
>>> are you sure that your machine didn't just run out ofmemory?
>>> The recon-all.log file includes the amount of free (nd total)
>>> memory at the time the process was started.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Thu, 5 Apr 2018, srishti goel wrote:
>>>
>>> Hi,
>>> I have been trying to edit structural brains and
>>> very few times I would get the following error whie
>>> running recon-all -s
>>> subjID
>>>
>>> white matter peak found at 110
>>> cannot allocate memory
>>>
>>> Upon looking at the archive, there was only one
>>> similar issue and it was recommend to check mri_info
>>> as the brain mask might
>>> have been corrupted. I did that and here is the
>>> output:
>>>
>>> Volume information for brainmask.mgz
>>>
>>> type: MGH
>>>
>>> dimensins: 256 x 256 x 256
>>>
>>> voxel sizes: 1.000000, 1.00000, 1.000000
>>>
>>> type: UCHAR (0)
>>>
>>> fov: 256.000
>>>
>>> dof: 0
>>>
>>> xstart: -128.0, xend: 128.0
>>>
>>> ystart: -128.0, yend: 128.0
>>>
>>> zstart: -128.0, zend: 128.0
>>>
>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00
>>> msec, flip angle:0.00 degrees
>>>
>>> nframes: 1
>>>
>>> PhEncDir: UNKNOWN
>>>
>>> FieldStrength: 0.000000
>>>
>>> ras xform present
>>>
>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r
>>> = 0.0000, c_r = -1.0000
>>>
>>> : x_a = 0.0000, y_a = 0.0000, z_a
>>> = .0000, c_a = 37.5000
>>>
>>> : x_s = 0.0000, y_s = -1.0000, z_s
>>> = 0.0000, c_s = 4.7185
>>>
>>>
>>> talairach xfm :/pine/scr/s/r/srishtig/Duke_T
>>> est/Freesurfer_out/11039/mri/transforms/talair
>>> ach.xfm
>>>
>>> Orientation : LIA
>>>
>>> Primary Slice Direction: coronal
>>>
>>>
>>> voxel to ras transform:
>>>
>>> -1.0000 0.0000 0.0000 127.0000
>>>
>>> 0.0000 0.0000 1.0000 -90.5000
>>>
>>> 0.0000 -1.0000 0.0000 132.7185
>>>
>>> 0.0000 0.0000 0.0000 1.0000
>>>
>>>
>>> voxel-to-ras determinant -1
>>>
>>>
>>> ras to voxel transform:
>>>
>>> -1.0000 -0.0000 -0.0000 127.0000
>>>
>>> -0.0000 -0.0000 -1.0000 132.7185
>>>
>>> -0.0000 1.0000 -0.0000 90.5000
>>>
>>> -0.0000 -0.0000 -0.0000 1.0000
>>>
>>>
>>> Is there any other way to resolve this issue than
>>> reconstruction the brain again and doing all the
>>> edits all over again hoping
>>> that the brain mask does not get corrupted this
>>> time?
>>>
>>> Appreciate any help with this.
>>>
>>> Best,
>>> Srishti
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
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>------------------------------
>
>Message: 7
>Date: Thu, 5 Apr 2018 12:31:43 -0400 (EDT)
>From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <alpine.lrh.2.21.1804051231080.18...@tiamat.nmr.mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Srishti
>
>if you look in the subject's scripts dir there should be a file named
>"recon-all.cmd". Try rerunning the last command in it (probably from the
>mri dir)
>
>cheers
>Bruce
>On Thu, 5 Apr 2018, srishti goel wrote:
>
>> I am sorry, I am not sure what do you mean by running the command line
>>directly?
>> I use the following command:
>>
>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>>srish...@email.unc.edu --wrap "export
>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>>recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa"
>>
>>
>> where sbatch..... until export is our local server submission command
>>and I run this command from the command line itself, not
>> using any script.
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu> wrote:
>> if you run the command that failed again on the command line
>>directly (that is, not in recon-all) does it fail
>> again?
>>
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi Bruce,
>>
>> The machine definitely hasn't run out of memory. Here is
>>the memory usage
>> from recon-all.log ?
>>
>> ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? ? ?used ? ? ? ?free ?
>>? ? ? ? ? ? ? ?
>> shared ?buff/cache ? available
>> Mem: ? ? ?263726968 ? ?34330048 ? 152102696 ? ? ? 12944 ?
>>?77294224 ?
>> 191963372
>> Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? ? ? ? ? 2097148
>>
>>
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu>
>> wrote:
>> ? ? ? Hi Srishti
>>
>> ? ? ? are you sure that your machine didn't just run out of
>>memory?
>> ? ? ? The recon-all.log file includes the amount of free
>>(and total)
>> ? ? ? memory at the time the process was started.
>>
>> ? ? ? cheers
>> ? ? ? Bruce
>>
>> ? ? ? ?On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> ? ? ? ? ? ? Hi,
>> ? ? ? ? ? ? I have been trying to edit structural brains and
>> ? ? ? ? ? ? very few times I would get the following error
>>while
>> ? ? ? ? ? ? running recon-all -s
>> ? ? ? ? ? ? subjID
>>
>> ? ? ? ? ? ? white matter peak found at 110
>> ? ? ? ? ? ? cannot allocate memory
>>
>> ? ? ? ? ? ? Upon looking at the archive, there was only one
>> ? ? ? ? ? ? similar issue and it was recommend to check
>>mri_info
>> ? ? ? ? ? ? as the brain mask might
>> ? ? ? ? ? ? have been corrupted. I did that and here is the
>> ? ? ? ? ? ? output:
>>
>> ? ? ? ? ? ? Volume information for brainmask.mgz
>>
>> ? ? ? ? ? ? ? ? ? ? ? type: MGH
>>
>> ? ? ? ? ? ? ? ? dimensions: 256 x 256 x 256
>>
>> ? ? ? ? ? ? ?? voxel sizes: 1.000000, 1.000000, 1.000000
>>
>> ? ? ? ? ? ? ? ? ? ? ? type: UCHAR (0)
>>
>> ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000
>>
>> ? ? ? ? ? ? ?? ? ? ? ? dof: 0
>>
>> ? ? ? ? ? ? ? ? ? ? xstart: -128.0, xend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ystart: -128.0, yend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? zstart: -128.0, zend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI:
>>0.00
>> ? ? ? ? ? ? msec, flip angle: 0.00 degrees
>>
>> ? ? ? ? ? ? ?? ? ? nframes: 1
>>
>> ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN
>>
>> ? ? ? ? ? ? ?? ? ? FieldStrength: 0.000000
>>
>> ? ? ? ? ? ? ras xform present
>>
>> ? ? ? ? ? ? ? ? xform info: x_r =? -1.0000, y_r = ? 0.0000,
>>z_r
>> ? ? ? ? ? ? = ? 0.0000, c_r =? ? -1.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ? 0.0000, y_a = ? 0.0000,
>>z_a
>> ? ? ? ? ? ? = ? 1.0000, c_a =? ? 37.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s =? -1.0000,
>>z_s
>> ? ? ? ? ? ? = ? 0.0000, c_s = ? ? 4.7185
>>
>>
>> ? ? ? ? ? ? talairach xfm
>>:/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tal
>>air
>> ? ? ? ? ? ? ach.xfm
>>
>> ? ? ? ? ? ? Orientation ? : LIA
>>
>> ? ? ? ? ? ? Primary Slice Direction: coronal
>>
>>
>> ? ? ? ? ? ? voxel to ras transform:
>>
>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? 0.0000 ?
>>127.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 1.0000 ?
>>-90.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? 0.0000 ?
>>132.7185
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? ?
>>1.0000
>>
>>
>> ? ? ? ? ? ? voxel-to-ras determinant -1
>>
>>
>> ? ? ? ? ? ? ras to voxel transform:
>>
>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000? -0.0000? -0.0000 ?
>>127.0000
>>
>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000? -1.0000 ?
>>132.7185
>>
>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000 ? 1.0000? -0.0000? ?
>>90.5000
>>
>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000? -0.0000 ? ?
>>1.0000
>>
>>
>> ? ? ? ? ? ? Is there any other way to resolve this issue
>>than
>> ? ? ? ? ? ? reconstruction the brain again and doing all the
>> ? ? ? ? ? ? edits all over again hoping
>> ? ? ? ? ? ? that the?brain mask does not get corrupted this
>> ? ? ? ? ? ? time?
>>
>> ? ? ? ? ? ? Appreciate any help with this.
>>
>> ? ? ? ? ? ? Best,
>> ? ? ? ? ? ? Srishti
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the
>>person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in
>>error and the
>> e-mail
>> contains patient information, please contact the Partners
>>Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was
>>sent to you
>> in error
>> but does not contain patient information, please contact
>>the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>>
>>
>>
>>
>
>------------------------------
>
>Message: 8
>Date: Thu, 5 Apr 2018 12:41:49 -0400
>From: srishti goel <23srishtig...@gmail.com>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <CAGqM=ZhW7-+qbR3szJv+znAPa=ZVZ9Npexz4Fu2=frnsijb...@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Should I re-run the recon-all after running the last command from
>recon-all.cmd?
>
>Best,
>Srishti
>Social/Clinical Research Specialist
>Child Imaging Research and Life Experiences Lab
>University of North Carolina at Chapel Hill
>email (W): srish...@email.unc.edu
>skype: srishti.goel12
>
>
>On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>wrote:
>
>> Hi Srishti
>>
>> if you look in the subject's scripts dir there should be a file named
>> "recon-all.cmd". Try rerunning the last command in it (probably from the
>> mri dir)
>>
>>
>> cheers
>> Bruce
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> I am sorry, I am not sure what do you mean by running the command line
>>> directly?
>>> I use the following command:
>>>
>>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>>> srish...@email.unc.edu --wrap "export
>>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>>> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa"
>>>
>>>
>>> where sbatch..... until export is our local server submission command
>>>and
>>> I run this command from the command line itself, not
>>> using any script.
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl
>>><fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>> if you run the command that failed again on the command line
>>> directly (that is, not in recon-all) does it fail
>>> again?
>>>
>>> On Thu, 5 Apr 2018, srishti goel wrote:
>>>
>>> Hi Bruce,
>>>
>>> The machine definitely hasn't run out of memory. Here is
>>>the
>>> memory usage
>>> from recon-all.log
>>>
>>> total used free
>>>
>>> shared buff/cache available
>>> Mem: 263726968 34330048 152102696 12944
>>> 77294224
>>> 191963372
>>> Swap: 2097148 0 2097148
>>>
>>>
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>> Hi Srishti
>>>
>>> are you sure that your machine didn't just run out of
>>> memory?
>>> The recon-all.log file includes the amount of free
>>>(and
>>> total)
>>> memory at the time the process was started.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Thu, 5 Apr 2018, srishti goel wrote:
>>>
>>> Hi,
>>> I have been trying to edit structural brains
>>>and
>>> very few times I would get the following error
>>> while
>>> running recon-all -s
>>> subjID
>>>
>>> white matter peak found at 110
>>> cannot allocate memory
>>>
>>> Upon looking at the archive, there was only one
>>> similar issue and it was recommend to check
>>> mri_info
>>> as the brain mask might
>>> have been corrupted. I did that and here is the
>>> output:
>>>
>>> Volume information for brainmask.mgz
>>>
>>> type: MGH
>>>
>>> dimensions: 256 x 256 x 256
>>>
>>> voxel sizes: 1.000000, 1.000000, 1.000000
>>>
>>> type: UCHAR (0)
>>>
>>> fov: 256.000
>>>
>>> dof: 0
>>>
>>> xstart: -128.0, xend: 128.0
>>>
>>> ystart: -128.0, yend: 128.0
>>>
>>> zstart: -128.0, zend: 128.0
>>>
>>> TR: 0.00 msec, TE: 0.00 msec, TI:
>>>0.00
>>> msec, flip angle: 0.00 degrees
>>>
>>> nframes: 1
>>>
>>> PhEncDir: UNKNOWN
>>>
>>> FieldStrength: 0.000000
>>>
>>> ras xform present
>>>
>>> xform info: x_r = -1.0000, y_r = 0.0000,
>>> z_r
>>> = 0.0000, c_r = -1.0000
>>>
>>> : x_a = 0.0000, y_a = 0.0000,
>>> z_a
>>> = 1.0000, c_a = 37.5000
>>>
>>> : x_s = 0.0000, y_s = -1.0000,
>>> z_s
>>> = 0.0000, c_s = 4.7185
>>>
>>>
>>> talairach xfm :/pine/scr/s/r/srishtig/Duke_T
>>> est/Freesurfer_out/11039/mri/transforms/talair
>>> ach.xfm
>>>
>>> Orientation : LIA
>>>
>>> Primary Slice Direction: coronal
>>>
>>>
>>> voxel to ras transform:
>>>
>>> -1.0000 0.0000 0.0000
>>> 127.0000
>>>
>>> 0.0000 0.0000 1.0000
>>> -90.5000
>>>
>>> 0.0000 -1.0000 0.0000
>>> 132.7185
>>>
>>> 0.0000 0.0000 0.0000
>>> 1.0000
>>>
>>>
>>> voxel-to-ras determinant -1
>>>
>>>
>>> ras to voxel transform:
>>>
>>> -1.0000 -0.0000 -0.0000
>>> 127.0000
>>>
>>> -0.0000 -0.0000 -1.0000
>>> 132.7185
>>>
>>> -0.0000 1.0000 -0.0000
>>> 90.5000
>>>
>>> -0.0000 -0.0000 -0.0000
>>> 1.0000
>>>
>>>
>>> Is there any other way to resolve this issue
>>>than
>>> reconstruction the brain again and doing all
>>>the
>>> edits all over again hoping
>>> that the brain mask does not get corrupted this
>>> time?
>>>
>>> Appreciate any help with this.
>>>
>>> Best,
>>> Srishti
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>>
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the
>>> person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in
>>> error and the
>>> e-mail
>>> contains patient information, please contact the Partners
>>> Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was
>>> sent to you
>>> in error
>>> but does not contain patient information, please contact
>>>the
>>> sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>>it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
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>------------------------------
>
>Message: 9
>Date: Thu, 5 Apr 2018 12:43:22 -0400 (EDT)
>From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <alpine.lrh.2.21.1804051243000.18...@tiamat.nmr.mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"
>
>let's see if it works. If it does, you should be able to run
>
>recon-all -s SUBJID -make all
>
>cheers
>Bruce
>
>
>On Thu, 5 Apr 2018, srishti goel wrote:
>
>> Should I re-run the recon-all after running the last command from
>>recon-all.cmd?
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu> wrote:
>> Hi Srishti
>>
>> if you look in the subject's scripts dir there should be a file
>>named "recon-all.cmd". Try rerunning the last
>> command in it (probably from the mri dir)
>>
>> cheers
>> Bruce
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> I am sorry, I am not sure what do you mean by running the
>>command line directly?
>> I use the following command:
>>
>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>>srish...@email.unc.edu --wrap "export
>>
>>SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>>recon-all -s 13166
>> -autorecon2-cp -autorecon3 -nowmsa"
>>
>>
>> where sbatch..... until export is our local server
>>submission command and I run this command from the
>> command line itself, not
>> using any script.
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu> wrote:
>> ? ? ? if you run the command that failed again on the
>>command line directly (that is, not in
>> recon-all) does it fail
>> ? ? ? again?
>>
>> ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> ? ? ? ? ? ? Hi Bruce,
>>
>> ? ? ? ? ? ? The machine definitely hasn't run out of
>>memory. Here is the memory usage
>> ? ? ? ? ? ? from recon-all.log ?
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? ? ?used ?
>>? ? ?free ? ? ? ? ? ? ? ? ?
>> ? ? ? ? ? ? shared ?buff/cache ? available
>> ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ? 152102696 ? ?
>>? 12944 ? ?77294224 ?
>> ? ? ? ? ? ? 191963372
>> ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? ? ? ? ?
>>2097148
>>
>>
>>
>>
>> ? ? ? ? ? ? Best,
>> ? ? ? ? ? ? Srishti
>> ? ? ? ? ? ? Social/Clinical Research Specialist
>> ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab
>> ? ? ? ? ? ? University of North Carolina at Chapel Hill
>> ? ? ? ? ? ? email (W): srish...@email.unc.edu
>> ? ? ? ? ? ? skype: srishti.goel12
>>
>>
>> ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu>
>> ? ? ? ? ? ? wrote:
>> ? ? ? ? ? ? ? ? ? Hi Srishti
>>
>> ? ? ? ? ? ? ? ? ? are you sure that your machine didn't
>>just run out of memory?
>> ? ? ? ? ? ? ? ? ? The recon-all.log file includes the
>>amount of free (and total)
>> ? ? ? ? ? ? ? ? ? memory at the time the process was
>>started.
>>
>> ? ? ? ? ? ? ? ? ? cheers
>> ? ? ? ? ? ? ? ? ? Bruce
>>
>> ? ? ? ? ? ? ? ? ? ?On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Hi,
>> ? ? ? ? ? ? ? ? ? ? ? ? I have been trying to edit
>>structural brains and
>> ? ? ? ? ? ? ? ? ? ? ? ? very few times I would get the
>>following error while
>> ? ? ? ? ? ? ? ? ? ? ? ? running recon-all -s
>> ? ? ? ? ? ? ? ? ? ? ? ? subjID
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? white matter peak found at 110
>> ? ? ? ? ? ? ? ? ? ? ? ? cannot allocate memory
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Upon looking at the archive, there
>>was only one
>> ? ? ? ? ? ? ? ? ? ? ? ? similar issue and it was recommend
>>to check mri_info
>> ? ? ? ? ? ? ? ? ? ? ? ? as the brain mask might
>> ? ? ? ? ? ? ? ? ? ? ? ? have been corrupted. I did that and
>>here is the
>> ? ? ? ? ? ? ? ? ? ? ? ? output:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Volume information for brainmask.mgz
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: MGH
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? dimensions: 256 x 256 x 256
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? voxel sizes: 1.000000, 1.000000,
>>1.000000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: UCHAR (0)
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? dof: 0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xstart: -128.0, xend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ystart: -128.0, yend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? zstart: -128.0, zend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00
>>msec, TI: 0.00
>> ? ? ? ? ? ? ? ? ? ? ? ? msec, flip angle: 0.00 degrees
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? nframes: 1
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? FieldStrength: 0.000000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ras xform present
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? xform info: x_r =? -1.0000, y_r
>>= ? 0.0000, z_r
>> ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_r =? ? -1.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ? 0.0000, y_a
>>= ? 0.0000, z_a
>> ? ? ? ? ? ? ? ? ? ? ? ? = ? 1.0000, c_a =? ? 37.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s
>>=? -1.0000, z_s
>> ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_s = ? ? 4.7185
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? talairach xfm
>>
>>:/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tal
>>air
>> ? ? ? ? ? ? ? ? ? ? ? ? ach.xfm
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Orientation ? : LIA
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Primary Slice Direction: coronal
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? voxel to ras transform:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ?
>>0.0000 ? 127.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ?
>>1.0000 ? -90.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000? -1.0000 ?
>>0.0000 ? 132.7185
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ?
>>0.0000 ? ? 1.0000
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? voxel-to-ras determinant -1
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ras to voxel transform:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000? -0.0000?
>>-0.0000 ? 127.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000?
>>-1.0000 ? 132.7185
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000 ? 1.0000?
>>-0.0000? ? 90.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000?
>>-0.0000 ? ? 1.0000
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Is there any other way to resolve
>>this issue than
>> ? ? ? ? ? ? ? ? ? ? ? ? reconstruction the brain again and
>>doing all the
>> ? ? ? ? ? ? ? ? ? ? ? ? edits all over again hoping
>> ? ? ? ? ? ? ? ? ? ? ? ? that the?brain mask does not get
>>corrupted this
>> ? ? ? ? ? ? ? ? ? ? ? ? time?
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Appreciate any help with this.
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Best,
>> ? ? ? ? ? ? ? ? ? ? ? ? Srishti
>>
>>
>> ? ? ? ? ? ? _______________________________________________
>> ? ? ? ? ? ? Freesurfer mailing list
>> ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu
>> ? ? ? ? ? ?
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ? ? ? ? ? ? The information in this e-mail is intended only
>>for the person to whom
>> ? ? ? ? ? ? it is
>> ? ? ? ? ? ? addressed. If you believe this e-mail was sent
>>to you in error and the
>> ? ? ? ? ? ? e-mail
>> ? ? ? ? ? ? contains patient information, please contact
>>the Partners Compliance
>> ? ? ? ? ? ? HelpLine at
>> ? ? ? ? ? ? http://www.partners.org/complianceline . If the
>>e-mail was sent to you
>> ? ? ? ? ? ? in error
>> ? ? ? ? ? ? but does not contain patient information,
>>please contact the sender
>> ? ? ? ? ? ? and properly
>> ? ? ? ? ? ? dispose of the e-mail.
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the
>>person to whom it is
>> addressed. If you believe this e-mail was sent to you in
>>error and the e-mail
>> contains patient information, please contact the Partners
>>Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was
>>sent to you in error
>> but does not contain patient information, please contact
>>the sender and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>>
>>
>>
>>
>
>------------------------------
>
>Message: 10
>Date: Thu, 5 Apr 2018 12:46:40 -0400
>From: srishti goel <23srishtig...@gmail.com>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <CAGqM=zi0ousz8xx5+olejhh_8xknnhjsoem48qogydhhyh3...@mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>So it gave this error:
>
>3d normalization pass 1 of 2
>
>white matter peak found at 110
>
>HISTOalloc(-2147483648): could not allocate histogram
>
>Cannot allocate memory
>
>Best,
>Srishti
>Social/Clinical Research Specialist
>Child Imaging Research and Life Experiences Lab
>University of North Carolina at Chapel Hill
>email (W): srish...@email.unc.edu
>skype: srishti.goel12
>
>
>On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>wrote:
>
>> let's see if it works. If it does, you should be able to run
>>
>> recon-all -s SUBJID -make all
>>
>>
>> cheers
>> Bruce
>>
>>
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Should I re-run the recon-all after running the last command from
>>> recon-all.cmd?
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl
>>><fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>> Hi Srishti
>>>
>>> if you look in the subject's scripts dir there should be a file
>>> named "recon-all.cmd". Try rerunning the last
>>> command in it (probably from the mri dir)
>>>
>>> cheers
>>> Bruce
>>> On Thu, 5 Apr 2018, srishti goel wrote:
>>>
>>> I am sorry, I am not sure what do you mean by running the
>>> command line directly?
>>> I use the following command:
>>>
>>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>>> srish...@email.unc.edu --wrap "export
>>>
>>>SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>>> recon-all -s 13166
>>> -autorecon2-cp -autorecon3 -nowmsa"
>>>
>>>
>>> where sbatch..... until export is our local server
>>>submission
>>> command and I run this command from the
>>> command line itself, not
>>> using any script.
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> if you run the command that failed again on the
>>>command
>>> line directly (that is, not in
>>> recon-all) does it fail
>>> again?
>>>
>>> On Thu, 5 Apr 2018, srishti goel wrote:
>>>
>>> Hi Bruce,
>>>
>>> The machine definitely hasn't run out of
>>>memory.
>>> Here is the memory usage
>>> from recon-all.log
>>>
>>> total used
>>> free
>>> shared buff/cache available
>>> Mem: 263726968 34330048 152102696
>>> 12944 77294224
>>> 191963372
>>> Swap: 2097148 0
>>> 2097148
>>>
>>>
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>> Hi Srishti
>>>
>>> are you sure that your machine didn't
>>>just
>>> run out of memory?
>>> The recon-all.log file includes the
>>>amount
>>> of free (and total)
>>> memory at the time the process was
>>>started.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Thu, 5 Apr 2018, srishti goel wrote:
>>>
>>> Hi,
>>> I have been trying to edit
>>>structural
>>> brains and
>>> very few times I would get the
>>> following error while
>>> running recon-all -s
>>> subjID
>>>
>>> white matter peak found at 110
>>> cannot allocate memory
>>>
>>> Upon looking at the archive, there
>>> was only one
>>> similar issue and it was recommend
>>>to
>>> check mri_info
>>> as the brain mask might
>>> have been corrupted. I did that and
>>> here is the
>>> output:
>>>
>>> Volume information for
>>>brainmask.mgz
>>>
>>> type: MGH
>>>
>>> dimensions: 256 x 256 x 256
>>>
>>> voxel sizes: 1.000000, 1.000000,
>>> 1.000000
>>>
>>> type: UCHAR (0)
>>>
>>> fov: 256.000
>>>
>>> dof: 0
>>>
>>> xstart: -128.0, xend: 128.0
>>>
>>> ystart: -128.0, yend: 128.0
>>>
>>> zstart: -128.0, zend: 128.0
>>>
>>> TR: 0.00 msec, TE: 0.00
>>> msec, TI: 0.00
>>> msec, flip angle: 0.00 degrees
>>>
>>> nframes: 1
>>>
>>> PhEncDir: UNKNOWN
>>>
>>> FieldStrength: 0.000000
>>>
>>> ras xform present
>>>
>>> xform info: x_r = -1.0000,
>>>y_r =
>>> 0.0000, z_r
>>> = 0.0000, c_r = -1.0000
>>>
>>> : x_a = 0.0000,
>>>y_a =
>>> 0.0000, z_a
>>> = 1.0000, c_a = 37.5000
>>>
>>> : x_s = 0.0000, y_s
>>> = -1.0000, z_s
>>> = 0.0000, c_s = 4.7185
>>>
>>>
>>> talairach xfm
>>>
>>>:/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/t
>>> ransforms/talair
>>> ach.xfm
>>>
>>> Orientation : LIA
>>>
>>> Primary Slice Direction: coronal
>>>
>>>
>>> voxel to ras transform:
>>>
>>> -1.0000 0.0000
>>> 0.0000 127.0000
>>>
>>> 0.0000 0.0000
>>> 1.0000 -90.5000
>>>
>>> 0.0000 -1.0000
>>> 0.0000 132.7185
>>>
>>> 0.0000 0.0000
>>> 0.0000 1.0000
>>>
>>>
>>> voxel-to-ras determinant -1
>>>
>>>
>>> ras to voxel transform:
>>>
>>> -1.0000 -0.0000
>>> -0.0000 127.0000
>>>
>>> -0.0000 -0.0000
>>> -1.0000 132.7185
>>>
>>> -0.0000 1.0000
>>> -0.0000 90.5000
>>>
>>> -0.0000 -0.0000
>>> -0.0000 1.0000
>>>
>>>
>>> Is there any other way to resolve
>>> this issue than
>>> reconstruction the brain again and
>>> doing all the
>>> edits all over again hoping
>>> that the brain mask does not get
>>> corrupted this
>>> time?
>>>
>>> Appreciate any help with this.
>>>
>>> Best,
>>> Srishti
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.e
>>> du/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only
>>> for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent
>>>to
>>> you in error and the
>>> e-mail
>>> contains patient information, please contact
>>>the
>>> Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the
>>> e-mail was sent to you
>>> in error
>>> but does not contain patient information,
>>>please
>>> contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>>
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the
>>> person to whom it is
>>> addressed. If you believe this e-mail was sent to you in
>>> error and the e-mail
>>> contains patient information, please contact the Partners
>>> Compliance HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was
>>> sent to you in error
>>> but does not contain patient information, please contact
>>>the
>>> sender and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>>it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>>it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
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>
>------------------------------
>
>Message: 11
>Date: Thu, 5 Apr 2018 12:48:08 -0400 (EDT)
>From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
> peak at 110, cannot allocate memory)
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
> <alpine.lrh.2.21.1804051247570.18...@tiamat.nmr.mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"
>
>can you email us the input file and the full command line you ran?
>On Thu, 5
>Apr 2018, srishti goel wrote:
>
>> So it gave this error:
>>
>> 3d normalization pass 1 of 2
>>
>> white matter peak found at 110
>>
>> HISTOalloc(-2147483648): could not allocate histogram
>>
>> Cannot allocate memory
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu> wrote:
>> let's see if it works. If it does, you should be able to run
>>
>> recon-all -s SUBJID -make all
>>
>> cheers
>> Bruce
>>
>>
>> On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Should I re-run the recon-all after running the last
>>command from recon-all.cmd?
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu> wrote:
>> ? ? ? Hi Srishti
>>
>> ? ? ? if you look in the subject's scripts dir there should
>>be a file named "recon-all.cmd". Try
>> rerunning the last
>> ? ? ? command in it (probably from the mri dir)
>>
>> ? ? ? cheers
>> ? ? ? Bruce
>> ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> ? ? ? ? ? ? I am sorry, I am not sure what do you mean by
>>running the command line directly?
>> ? ? ? ? ? ? I use the following command:
>>
>> ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00 --mail-type END
>>--mail-user srish...@email.unc.edu --wrap
>> "export
>> ? ? ? ? ? ?
>>SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>>recon-all -s 13166
>> ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa"
>>
>>
>> ? ? ? ? ? ? where sbatch..... until export is our local
>>server submission command and I run this
>> command from the
>> ? ? ? ? ? ? command line itself, not
>> ? ? ? ? ? ? using any script.
>>
>>
>> ? ? ? ? ? ? Best,
>> ? ? ? ? ? ? Srishti
>> ? ? ? ? ? ? Social/Clinical Research Specialist
>> ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab
>> ? ? ? ? ? ? University of North Carolina at Chapel Hill
>> ? ? ? ? ? ? email (W): srish...@email.unc.edu
>> ? ? ? ? ? ? skype: srishti.goel12
>>
>>
>> ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl
>><fis...@nmr.mgh.harvard.edu> wrote:
>> ? ? ? ? ? ? ? ? ? if you run the command that failed again
>>on the command line directly (that is, not
>> in
>> ? ? ? ? ? ? recon-all) does it fail
>> ? ? ? ? ? ? ? ? ? again?
>>
>> ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce,
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely hasn't run
>>out of memory. Here is the memory usage
>> ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ?
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ?
>>? ? ?used ? ? ? ?free ? ? ? ? ? ? ? ? ?
>> ? ? ? ? ? ? ? ? ? ? ? ? shared ?buff/cache ? available
>> ? ? ? ? ? ? ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ?
>>152102696 ? ? ? 12944 ? ?77294224 ?
>> ? ? ? ? ? ? ? ? ? ? ? ? 191963372
>> ? ? ? ? ? ? ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ?
>>? ? ? ? 2097148
>>
>>
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? Best,
>> ? ? ? ? ? ? ? ? ? ? ? ? Srishti
>> ? ? ? ? ? ? ? ? ? ? ? ? Social/Clinical Research Specialist
>> ? ? ? ? ? ? ? ? ? ? ? ? Child Imaging Research and Life
>>Experiences Lab
>> ? ? ? ? ? ? ? ? ? ? ? ? University of North Carolina at
>>Chapel Hill
>> ? ? ? ? ? ? ? ? ? ? ? ? email (W): srish...@email.unc.edu
>> ? ? ? ? ? ? ? ? ? ? ? ? skype: srishti.goel12
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:16 PM,
>>Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> ? ? ? ? ? ? ? ? ? ? ? ? wrote:
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Srishti
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? are you sure that your
>>machine didn't just run out of memory?
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? The recon-all.log file
>>includes the amount of free (and total)
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? memory at the time the
>>process was started.
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? cheers
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Bruce
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?On Thu, 5 Apr 2018, srishti
>>goel wrote:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I have been trying to
>>edit structural brains and
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? very few times I would
>>get the following error while
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? running recon-all -s
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? subjID
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? white matter peak found
>>at 110
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? cannot allocate memory
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Upon looking at the
>>archive, there was only one
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? similar issue and it
>>was recommend to check mri_info
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? as the brain mask might
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? have been corrupted. I
>>did that and here is the
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? output:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Volume information for
>>brainmask.mgz
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: MGH
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? dimensions: 256 x
>>256 x 256
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? voxel sizes:
>>1.000000, 1.000000, 1.000000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: UCHAR
>>(0)
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? dof: 0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xstart: -128.0,
>>xend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ystart: -128.0,
>>yend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? zstart: -128.0,
>>zend: 128.0
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00
>>msec, TE: 0.00 msec, TI: 0.00
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? msec, flip angle: 0.00
>>degrees
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? nframes: 1
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? FieldStrength:
>>0.000000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ras xform present
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xform info: x_r =?
>>-1.0000, y_r = ? 0.0000, z_r
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_r =? ?
>>-1.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ?
>>0.0000, y_a = ? 0.0000, z_a
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 1.0000, c_a =? ?
>>37.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ?
>>0.0000, y_s =? -1.0000, z_s
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_s = ? ?
>>4.7185
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? talairach xfm
>> ? ? ? ? ? ?
>>:/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tal
>>air
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ach.xfm
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Orientation ? : LIA
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Primary Slice
>>Direction: coronal
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? voxel to ras transform:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000
>>? 0.0000 ? 0.0000 ? 127.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000
>>? 0.0000 ? 1.0000 ? -90.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000?
>>-1.0000 ? 0.0000 ? 132.7185
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000
>>? 0.0000 ? 0.0000 ? ? 1.0000
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? voxel-to-ras
>>determinant -1
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ras to voxel transform:
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000?
>>-0.0000? -0.0000 ? 127.0000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000?
>>-0.0000? -1.0000 ? 132.7185
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000
>>? 1.0000? -0.0000? ? 90.5000
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000?
>>-0.0000? -0.0000 ? ? 1.0000
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Is there any other way
>>to resolve this issue than
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? reconstruction the
>>brain again and doing all the
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? edits all over again
>>hoping
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? that the?brain mask
>>does not get corrupted this
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? time?
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Appreciate any help
>>with this.
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Best,
>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Srishti
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ?
>>_______________________________________________
>> ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer mailing list
>> ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu
>> ? ? ? ? ? ? ? ? ? ? ? ?
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ? ? ? ? ? ? ? ? ? ? ? ? The information in this e-mail is
>>intended only for the person to whom
>> ? ? ? ? ? ? ? ? ? ? ? ? it is
>> ? ? ? ? ? ? ? ? ? ? ? ? addressed. If you believe this
>>e-mail was sent to you in error and the
>> ? ? ? ? ? ? ? ? ? ? ? ? e-mail
>> ? ? ? ? ? ? ? ? ? ? ? ? contains patient information,
>>please contact the Partners Compliance
>> ? ? ? ? ? ? ? ? ? ? ? ? HelpLine at
>> ? ? ? ? ? ? ? ? ? ? ? ?
>>http://www.partners.org/complianceline . If the e-mail was sent to you
>> ? ? ? ? ? ? ? ? ? ? ? ? in error
>> ? ? ? ? ? ? ? ? ? ? ? ? but does not contain patient
>>information, please contact the sender
>> ? ? ? ? ? ? ? ? ? ? ? ? and properly
>> ? ? ? ? ? ? ? ? ? ? ? ? dispose of the e-mail.
>>
>>
>>
>>
>> ? ? ? ? ? ? _______________________________________________
>> ? ? ? ? ? ? Freesurfer mailing list
>> ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu
>> ? ? ? ? ? ?
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ? ? ? ? ? ? The information in this e-mail is intended only
>>for the person to whom it is
>> ? ? ? ? ? ? addressed. If you believe this e-mail was sent
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>> ? ? ? ? ? ? but does not contain patient information,
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>> The information in this e-mail is intended only for the
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>> addressed. If you believe this e-mail was sent to you in
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>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
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>
>------------------------------
>
>Message: 12
>Date: Thu, 5 Apr 2018 12:49:49 -0400
>From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
>Subject: Re: [Freesurfer] mri_vol2surf: unable to compare volume maps
>To: <freesurfer@nmr.mgh.harvard.edu>
>Message-ID: <6bb974cb-7874-6541-ee7c-b635d3037...@mgh.harvard.edu>
>Content-Type: text/plain; charset="utf-8"; format=flowed
>
>Those commands look ok. My suspicion goes to the use of --regheader. See
>whether the registration is ok with
>
>tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s
>mni152_subject --surfs --reg reg.deleteme.dat
>
>
>On 04/05/2018 08:34 AM, srishti goel wrote:
>> Hi,
>>
>> I am trying to compare my volume maps
>> (negative_allsocial_proportion.nii) to someone else's
>> (SN_like_cortical_lh.nii.gz) who have it on a surface
>> (mni152_subject). So I used the steps for mri_vol2surf command as
>> follows:
>>
>> Commands:
>> mri_vol2surf --src negative_allsocial_proportion.nii --regheader
>> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5
>> Then to view it:
>> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii
>> -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
>>
>> Everything ran fine and we didn't get any error but then while viewing
>> the files we could not see our map (neg_allsocail_lh.nii) on the
>> surface. This file seemed to work fine as it is not an empty file when
>> I checked the file size. However, when we view it using tksurfer it
>> does not show up as a highlighted portion on the surface. The
>> SN_like_cortical_lh.nii.gz file shows up just fine.
>>
>> Could someone please help me figure out what might have gone wrong here.
>>
>> Thanks so much!
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>------------------------------
>
>Message: 13
>Date: Thu, 5 Apr 2018 12:59:16 -0400
>From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
>Subject: Re: [Freesurfer] scan log generated by dcmunpack
>To: <freesurfer@nmr.mgh.harvard.edu>
>Message-ID: <22ecfa88-e463-169b-03c5-4c25ac224...@mgh.harvard.edu>
>Content-Type: text/plain; charset="windows-1252"; format=flowed
>
>It looks like there is something wrong with that dicom file/series
>because the pixel spacing is "unknown". Where did the dicoms from from?
>Have they been anonymized?
>
>
>On 04/05/2018 12:12 PM, Kan Ding wrote:
>> Hello:
>>
>> I am trying to unpack my DICOM folder and run recon-all. After
>> dcmunpack, I selected 301 to run recon-all. But the recon-all didn?t
>> go through. Please see the attached scan.log, recon-all.log,
>> error.log, and the pic of my DICOM folder.
>>
>> Thank you so much.
>>
>> Kan Ding, MD
>>
>> Assistant Professor- Department of Neurology and Neurotherapeutics
>>
>> UT Southwestern Medical Center at Dallas
>>
>> Tel: 214-648-9197
>>
>> Fax: 214-648-6320
>>
>>
>> ------------------------------------------------------------------------
>>
>> UTSouthwestern
>>
>> Medical Center
>>
>>
>> The future of medicine, today.
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>------------------------------
>
>Message: 14
>Date: Thu, 5 Apr 2018 17:49:11 +0000
>From: "Crawford, Anna" <crawf...@ccf.org>
>Subject: [Freesurfer] Time Series to Surface
>To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>Message-ID: <1522950551835.87...@ccf.org>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hello,
>
>I have a time series (.hdr/.img) that I want to overlay onto a surface,
>specifically the inflated surface from the anatomy. I suspect I have to
>use mri_vol2surf, which requires a source registration file. How do I get
>this file? Then once I have this file, will I be able to view step by
>step through the time series on the inflated volume?
>
>Thanks for your help,
>Anna
>
>
>
>===================================
>
>
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>------------------------------
>
>Message: 15
>Date: Thu, 5 Apr 2018 19:21:18 +0000
>From: "Lussier,Desiree" <desiree.luss...@ufl.edu>
>Subject: [Freesurfer] Tracula - Could not find satisfactory control
> point fit
>To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>Message-ID:
>
> <bn6pr22mb0228f1c6a278da29232cc6c3ff...@bn6pr22mb0228.namprd22.prod.outlo
>ok.com>
>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Dear Freesurfer experts,
>
>
>I have been trying run trac-all -prep on two subjects but it seems to be
>stuck on the priors pathway estimation. The following (with updated
>number of tries) keeps appearing in the terminal:
>
>
> WARN: Could not find satisfactory control point fit - try 288
> Finding center streamline
> INFO: Step is 5 voxels
> WARN: Turning off deviation check for center streamline
> INFO: Step is 5 voxels
> WARN: Turning off FA check for center streamline
> INFO: Step is 5 voxels
>
>
>I've attached the log here. Previous communications I've seen regarding
>this are years old and were solved by upgrading to 5.3. However, I'm
>already using the 64 bit 6.0.
>
>
>Advice regarding this situation would be greatly appreciated.
>
>
>Thank you,
>
>Desiree Lussier
>
>
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>------------------------------
>
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